\contentsline {chapter}{\numberline {1}Class Index}{1}{chapter.1}
\contentsline {section}{\numberline {1.1}Class Hierarchy}{1}{section.1.1}
\contentsline {chapter}{\numberline {2}Class Index}{3}{chapter.2}
\contentsline {section}{\numberline {2.1}Class List}{3}{section.2.1}
\contentsline {chapter}{\numberline {3}Class Documentation}{5}{chapter.3}
\contentsline {section}{\numberline {3.1}Cell Class Reference}{5}{section.3.1}
\contentsline {subsection}{\numberline {3.1.1}Constructor \& Destructor Documentation}{6}{subsection.3.1.1}
\contentsline {subsubsection}{\numberline {3.1.1.1}Cell}{6}{subsubsection.3.1.1.1}
\contentsline {subsubsection}{\numberline {3.1.1.2}$\sim $Cell}{6}{subsubsection.3.1.1.2}
\contentsline {subsection}{\numberline {3.1.2}Member Function Documentation}{6}{subsection.3.1.2}
\contentsline {subsubsection}{\numberline {3.1.2.1}addDNA}{6}{subsubsection.3.1.2.1}
\contentsline {subsubsection}{\numberline {3.1.2.2}addInteraction}{6}{subsubsection.3.1.2.2}
\contentsline {subsubsection}{\numberline {3.1.2.3}addInteraction}{6}{subsubsection.3.1.2.3}
\contentsline {subsubsection}{\numberline {3.1.2.4}addMRNA}{6}{subsubsection.3.1.2.4}
\contentsline {subsubsection}{\numberline {3.1.2.5}addProtein}{6}{subsubsection.3.1.2.5}
\contentsline {subsubsection}{\numberline {3.1.2.6}addProtein}{6}{subsubsection.3.1.2.6}
\contentsline {subsubsection}{\numberline {3.1.2.7}degRateChange}{6}{subsubsection.3.1.2.7}
\contentsline {subsubsection}{\numberline {3.1.2.8}fwdRateChange}{7}{subsubsection.3.1.2.8}
\contentsline {subsubsection}{\numberline {3.1.2.9}getCellID}{7}{subsubsection.3.1.2.9}
\contentsline {subsubsection}{\numberline {3.1.2.10}getScore}{7}{subsubsection.3.1.2.10}
\contentsline {subsubsection}{\numberline {3.1.2.11}histoneMod}{7}{subsubsection.3.1.2.11}
\contentsline {subsubsection}{\numberline {3.1.2.12}isComplexed}{7}{subsubsection.3.1.2.12}
\contentsline {subsubsection}{\numberline {3.1.2.13}newBasic}{7}{subsubsection.3.1.2.13}
\contentsline {subsubsection}{\numberline {3.1.2.14}newComplex}{7}{subsubsection.3.1.2.14}
\contentsline {subsubsection}{\numberline {3.1.2.15}newPostTransMod}{7}{subsubsection.3.1.2.15}
\contentsline {subsubsection}{\numberline {3.1.2.16}newPromoter}{7}{subsubsection.3.1.2.16}
\contentsline {subsubsection}{\numberline {3.1.2.17}nextGeneration}{7}{subsubsection.3.1.2.17}
\contentsline {subsubsection}{\numberline {3.1.2.18}revRateChange}{8}{subsubsection.3.1.2.18}
\contentsline {subsubsection}{\numberline {3.1.2.19}rungeKuttaEvaluate}{8}{subsubsection.3.1.2.19}
\contentsline {section}{\numberline {3.2}Concentration Struct Reference}{9}{section.3.2}
\contentsline {section}{\numberline {3.3}DNA Class Reference}{10}{section.3.3}
\contentsline {subsection}{\numberline {3.3.1}Constructor \& Destructor Documentation}{10}{subsection.3.3.1}
\contentsline {subsubsection}{\numberline {3.3.1.1}DNA}{10}{subsubsection.3.3.1.1}
\contentsline {subsubsection}{\numberline {3.3.1.2}$\sim $DNA}{10}{subsubsection.3.3.1.2}
\contentsline {section}{\numberline {3.4}Experiment Class Reference}{11}{section.3.4}
\contentsline {subsection}{\numberline {3.4.1}Constructor \& Destructor Documentation}{11}{subsection.3.4.1}
\contentsline {subsubsection}{\numberline {3.4.1.1}Experiment}{11}{subsubsection.3.4.1.1}
\contentsline {subsubsection}{\numberline {3.4.1.2}$\sim $Experiment}{11}{subsubsection.3.4.1.2}
\contentsline {subsection}{\numberline {3.4.2}Member Function Documentation}{11}{subsection.3.4.2}
\contentsline {subsubsection}{\numberline {3.4.2.1}start}{11}{subsubsection.3.4.2.1}
\contentsline {section}{\numberline {3.5}Interaction Class Reference}{12}{section.3.5}
\contentsline {subsection}{\numberline {3.5.1}Constructor \& Destructor Documentation}{12}{subsection.3.5.1}
\contentsline {subsubsection}{\numberline {3.5.1.1}Interaction}{12}{subsubsection.3.5.1.1}
\contentsline {subsubsection}{\numberline {3.5.1.2}Interaction}{12}{subsubsection.3.5.1.2}
\contentsline {subsubsection}{\numberline {3.5.1.3}$\sim $Interaction}{12}{subsubsection.3.5.1.3}
\contentsline {subsection}{\numberline {3.5.2}Member Function Documentation}{12}{subsection.3.5.2}
\contentsline {subsubsection}{\numberline {3.5.2.1}getProductFactor}{12}{subsubsection.3.5.2.1}
\contentsline {subsubsection}{\numberline {3.5.2.2}getRate}{12}{subsubsection.3.5.2.2}
\contentsline {subsubsection}{\numberline {3.5.2.3}getRate}{12}{subsubsection.3.5.2.3}
\contentsline {subsubsection}{\numberline {3.5.2.4}getSubstrateFactor}{13}{subsubsection.3.5.2.4}
\contentsline {subsubsection}{\numberline {3.5.2.5}getTerm}{13}{subsubsection.3.5.2.5}
\contentsline {subsubsection}{\numberline {3.5.2.6}setProductFactor}{13}{subsubsection.3.5.2.6}
\contentsline {subsubsection}{\numberline {3.5.2.7}setRate}{13}{subsubsection.3.5.2.7}
\contentsline {section}{\numberline {3.6}Molecule Class Reference}{14}{section.3.6}
\contentsline {subsection}{\numberline {3.6.1}Constructor \& Destructor Documentation}{14}{subsection.3.6.1}
\contentsline {subsubsection}{\numberline {3.6.1.1}Molecule}{14}{subsubsection.3.6.1.1}
\contentsline {subsubsection}{\numberline {3.6.1.2}$\sim $Molecule}{15}{subsubsection.3.6.1.2}
\contentsline {subsection}{\numberline {3.6.2}Member Function Documentation}{15}{subsection.3.6.2}
\contentsline {subsubsection}{\numberline {3.6.2.1}getConcentration}{15}{subsubsection.3.6.2.1}
\contentsline {subsubsection}{\numberline {3.6.2.2}getInitialConcentration}{15}{subsubsection.3.6.2.2}
\contentsline {subsubsection}{\numberline {3.6.2.3}getMoleculeID}{15}{subsubsection.3.6.2.3}
\contentsline {section}{\numberline {3.7}MRNA Class Reference}{16}{section.3.7}
\contentsline {subsection}{\numberline {3.7.1}Constructor \& Destructor Documentation}{16}{subsection.3.7.1}
\contentsline {subsubsection}{\numberline {3.7.1.1}MRNA}{16}{subsubsection.3.7.1.1}
\contentsline {subsubsection}{\numberline {3.7.1.2}$\sim $MRNA}{16}{subsubsection.3.7.1.2}
\contentsline {section}{\numberline {3.8}MTRand Class Reference}{17}{section.3.8}
\contentsline {section}{\numberline {3.9}Protein Class Reference}{19}{section.3.9}
\contentsline {subsection}{\numberline {3.9.1}Constructor \& Destructor Documentation}{19}{subsection.3.9.1}
\contentsline {subsubsection}{\numberline {3.9.1.1}Protein}{19}{subsubsection.3.9.1.1}
\contentsline {subsubsection}{\numberline {3.9.1.2}$\sim $Protein}{19}{subsubsection.3.9.1.2}
\contentsline {subsection}{\numberline {3.9.2}Member Function Documentation}{19}{subsection.3.9.2}
\contentsline {subsubsection}{\numberline {3.9.2.1}getPostTransModCount}{19}{subsubsection.3.9.2.1}
\contentsline {section}{\numberline {3.10}Quantity Struct Reference}{20}{section.3.10}
\contentsline {section}{\numberline {3.11}Term Class Reference}{21}{section.3.11}
\contentsline {subsection}{\numberline {3.11.1}Detailed Description}{21}{subsection.3.11.1}
\contentsline {subsection}{\numberline {3.11.2}Constructor \& Destructor Documentation}{21}{subsection.3.11.2}
\contentsline {subsubsection}{\numberline {3.11.2.1}Term}{21}{subsubsection.3.11.2.1}
\contentsline {subsubsection}{\numberline {3.11.2.2}Term}{21}{subsubsection.3.11.2.2}
\contentsline {subsubsection}{\numberline {3.11.2.3}Term}{21}{subsubsection.3.11.2.3}
\contentsline {subsubsection}{\numberline {3.11.2.4}$\sim $Term}{21}{subsubsection.3.11.2.4}
\contentsline {subsection}{\numberline {3.11.3}Member Function Documentation}{22}{subsection.3.11.3}
\contentsline {subsubsection}{\numberline {3.11.3.1}addFactor}{22}{subsubsection.3.11.3.1}
\contentsline {subsubsection}{\numberline {3.11.3.2}getValue}{22}{subsubsection.3.11.3.2}
\contentsline {subsubsection}{\numberline {3.11.3.3}getValue}{22}{subsubsection.3.11.3.3}
\contentsline {subsubsection}{\numberline {3.11.3.4}setFactor}{22}{subsubsection.3.11.3.4}
